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While GENESIS is one of the most widely used simulation systems for computational biology, all such systems must continually adapt to changing technology, and changes in the knowledge base, capabilities, expectations and needs of its users. With biological modeling in particular, the large scale growth in the field has meant that researchers are addressing ever more sophisticated questions with ever more sophisticated models. Anticipating and then meeting these requirements is a vital part of user support. This section describes several efforts to be supported with this grant that are intended to provide additional ease in using the system.
Easing the Installation Process Because GENESIS is used on a wide variety of hardware platforms, each of which has a variety of operating system versions (e.g., SunOS and Solaris on Suns, and the many different versions of Linux and the associated GNU C libraries on PCs), GENESIS has traditionally been distributed in source form with compile and install instructions. However, users with limited computer experience have often experienced difficulties during the installation, resuling in a considerable drain on the GENESIS staff providing user support. Although email support will continue to be necessary, we will ease the installation process by developing "smart" auto-configuration scripts that will determine and set the necessary paths to library files, compilation options, and other necessary parameters. We will also provide a CD-ROM (with a downloadable image file on the GENESIS web site) that, when used to boot a PC running Windows, will run a version of Linux with GENESIS and its tutorials entirely from the CD-ROM. This should make GENESIS available to a much wider audience, during the transition to a version of GENESIS for MS Windows. Preliminary testing has shown that, although the speed of simulations is slower in this environment, it is nevertheless more than adequate to run the GENESIS tutorials on a low-end PC.
Continued development of special purpose interface tools. Included in the GENESIS system are a series of specialized interfaces intended to support the construction and evaluation of models at different levels of scale (c.f. Neurokit for single cells, and recently Kinetikit for biochemical kinetics modeling). The specific objective of these interfaces is to allow neurobiologists to construct and manipulate simulations with a minimum programming knowledge of the system. In principle, as the number of GENESIS objects already developed increases, more and more modelers can work at this level. This is likely to be particularly important to the growing interest in network and systems level simulations, which generally rely on existing single cell models. We therefore specifically propose to develop new specialize interfaces at the network and systems levels. As with the existing interfaces, these new "kits" will support a point and click interface for the construction and manipulation of models at each level. For example, NetKit will support the specification of connectivity, conduction velocities, and the choice of modeled neurons for network implementation. New tools will also be developed for visualizing the results of network simulations, and comparing simulated patterns of activity to those seen using single and multi-cell electrophysiology as well as with modern imaging techniques. As always with the development of "kits", the specific implementation will depend on strong interaction with both experimental and modeling users.
Continued development of systems for simulator interoperability. One of the major directions the GENESIS project has taken over the last several years, has been in the development of standards to allow simulator interoperability and database sharing (see http://www.genesis-sim.org/hbp/). This direction also anticipated the increased interest of modelers and experimentalists in examining interactions between different levels of biological scale. With support from this grant we will continue to interact with the group developing NeuroML ( http://www.neuroml.org), and the Systems Biology Workbench ( http://sbml.org/). This interaction will assure that these projects benefit from the experience and widespread use of GENESIS and also assure that GENESIS is integrated into whatever final systems are developed.